Ajout des obitools

Dockerfile

@@ -9,6 +9,9 @@ RUN apt-get update && apt-get install -y \
     libcurl4-openssl-dev \
     libssl-dev \
     libxml2-dev \
+    git \
+    build-essential \
+    curl \
     && apt-get clean && rm -rf /var/lib/apt/lists/*
 
 # Install R kernel for Jupyter (as root)
@@ -16,16 +19,29 @@ RUN R -e "install.packages('IRkernel', repos='http://cran.rstudio.com/')" && \
     R -e "IRkernel::installspec(user = FALSE)"
 
 # Install some useful R packages for labs
-RUN R -e "install.packages(c('ggplot2', 'dplyr', 'tidyr', 'readr'), repos='http://cran.rstudio.com/')"
+RUN R -e "install.packages(c('tidyverse', 'vegan', 'ade4'), repos='http://cran.rstudio.com/')"
 
 # Install bash kernel (as root also)
 RUN pip install bash_kernel && \
     python -m bash_kernel.install --sys-prefix
 
+# Install obitools4 (written in Go)
+RUN curl -L https://raw.githubusercontent.com/metabarcoding/obitools4/master/install_obitools.sh | bash
+
+# Install csvkit
+RUN pip install csvkit
+
+# Install csvlens
+RUN curl https://sh.rustup.rs -sSf | bash -s -- -y \
+    && . $HOME/.cargo/env \
+    && cargo install csvlens \
+    && mv $HOME/.cargo/bin/csvlens /usr/local/bin/ \
+    && rm -rf $HOME/.cargo $HOME/.rustup
+
 # Create necessary directories with proper permissions
 RUN mkdir -p /home/${NB_USER}/.local/share/jupyter && \
     chown -R ${NB_UID}:${NB_GID} /home/${NB_USER}
 
 USER ${NB_UID}
 
-WORKDIR /home/${NB_USER}
+WORKDIR /home/${NB_USER}